[2023-06-13 20:44:31,865] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:44:31,877] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:44:31,877] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference
[2023-06-13 20:44:33,029] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:44:33,032] [INFO] Task started: Prodigal
[2023-06-13 20:44:33,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg84e2920c-3e04-40a9-afd3-067c46da121b/GCA_022643695.1_ASM2264369v1_genomic.fna.gz | prodigal -d GCA_022643695.1_ASM2264369v1_genomic.fna/cds.fna -a GCA_022643695.1_ASM2264369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:44:37,847] [INFO] Task succeeded: Prodigal
[2023-06-13 20:44:37,847] [INFO] Task started: HMMsearch
[2023-06-13 20:44:37,847] [INFO] Running command: hmmsearch --tblout GCA_022643695.1_ASM2264369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/reference_markers.hmm GCA_022643695.1_ASM2264369v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:44:38,027] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:44:38,028] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg84e2920c-3e04-40a9-afd3-067c46da121b/GCA_022643695.1_ASM2264369v1_genomic.fna.gz]
[2023-06-13 20:44:38,049] [INFO] Query marker FASTA was written to GCA_022643695.1_ASM2264369v1_genomic.fna/markers.fasta
[2023-06-13 20:44:38,049] [INFO] Task started: Blastn
[2023-06-13 20:44:38,049] [INFO] Running command: blastn -query GCA_022643695.1_ASM2264369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/reference_markers.fasta -out GCA_022643695.1_ASM2264369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:38,578] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:38,581] [INFO] Selected 26 target genomes.
[2023-06-13 20:44:38,582] [INFO] Target genome list was writen to GCA_022643695.1_ASM2264369v1_genomic.fna/target_genomes.txt
[2023-06-13 20:44:38,585] [INFO] Task started: fastANI
[2023-06-13 20:44:38,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg84e2920c-3e04-40a9-afd3-067c46da121b/GCA_022643695.1_ASM2264369v1_genomic.fna.gz --refList GCA_022643695.1_ASM2264369v1_genomic.fna/target_genomes.txt --output GCA_022643695.1_ASM2264369v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:44:52,501] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:52,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:44:52,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:44:52,507] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 20:44:52,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 20:44:52,507] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	97.9094	527	614	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 20:44:52,508] [INFO] DFAST Taxonomy check result was written to GCA_022643695.1_ASM2264369v1_genomic.fna/tc_result.tsv
[2023-06-13 20:44:52,509] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:44:52,509] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:44:52,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/checkm_data
[2023-06-13 20:44:52,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:44:52,531] [INFO] Task started: CheckM
[2023-06-13 20:44:52,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022643695.1_ASM2264369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022643695.1_ASM2264369v1_genomic.fna/checkm_input GCA_022643695.1_ASM2264369v1_genomic.fna/checkm_result
[2023-06-13 20:45:12,672] [INFO] Task succeeded: CheckM
[2023-06-13 20:45:12,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:45:12,692] [INFO] ===== Completeness check finished =====
[2023-06-13 20:45:12,692] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:45:12,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022643695.1_ASM2264369v1_genomic.fna/markers.fasta)
[2023-06-13 20:45:12,693] [INFO] Task started: Blastn
[2023-06-13 20:45:12,693] [INFO] Running command: blastn -query GCA_022643695.1_ASM2264369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3add135-23c5-45ad-b82c-fad1b6fed3c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022643695.1_ASM2264369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:45:13,464] [INFO] Task succeeded: Blastn
[2023-06-13 20:45:13,468] [INFO] Selected 22 target genomes.
[2023-06-13 20:45:13,468] [INFO] Target genome list was writen to GCA_022643695.1_ASM2264369v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:45:13,473] [INFO] Task started: fastANI
[2023-06-13 20:45:13,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg84e2920c-3e04-40a9-afd3-067c46da121b/GCA_022643695.1_ASM2264369v1_genomic.fna.gz --refList GCA_022643695.1_ASM2264369v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022643695.1_ASM2264369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:45:22,121] [INFO] Task succeeded: fastANI
[2023-06-13 20:45:22,129] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:45:22,129] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900343155.1	s__Bulleidia massiliensis	97.8792	528	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.00	97.48	0.85	0.81	18	conclusive
GCA_900319505.1	s__Bulleidia sp900319505	77.9432	119	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.64	99.39	0.93	0.88	3	-
GCA_900315065.1	s__Bulleidia sp900315065	77.6462	108	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.99	99.99	0.97	0.97	2	-
GCF_009696165.1	s__Bulleidia intestinalis	77.2842	101	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	-
GCA_900314905.1	s__Bulleidia sp900314905	77.2146	78	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900770275.1	s__Bulleidia sp900770275	77.0362	67	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201565.1	s__Bulleidia sp905201565	76.7529	91	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539385.1	s__Bulleidia sp017539385	76.6979	70	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433125.1	s__Bulleidia sp017433125	76.6186	59	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_017543005.1	s__Bulleidia sp017543005	76.4035	62	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.24	98.24	0.79	0.79	2	-
GCA_900320455.1	s__Bulleidia sp900320455	76.1539	56	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.55	97.17	0.84	0.70	5	-
--------------------------------------------------------------------------------
[2023-06-13 20:45:22,131] [INFO] GTDB search result was written to GCA_022643695.1_ASM2264369v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:45:22,131] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:45:22,134] [INFO] DFAST_QC result json was written to GCA_022643695.1_ASM2264369v1_genomic.fna/dqc_result.json
[2023-06-13 20:45:22,134] [INFO] DFAST_QC completed!
[2023-06-13 20:45:22,134] [INFO] Total running time: 0h0m50s